Partial Molecular Characterization of Dahlia mosaic virus and Its Detection by PCR

Untangling the taxonomy of dahlia mosaic virus

In this brief note, we review the taxonomic history of dahlia mosaic virus (DMV) and related viruses. DMV is the only officially recognized caulimovirus known to infect dahlia (Dahlia variabilis) plants, although this virus appears to be relatively rare as a pathogen compared to a more recently described but unclassified caulimovirus called dahlia common mosaic virus (DCMV). We have undertaken a new set of analyses to test the hypothesis that DCMV represents a new caulimovirus species whose members infect dahlia, but we ultimately reject this hypothesis. A probable sequencing error was identified in the reference genome sequence of DMV, and consequently, we recommend that an alternative virus isolate be nominated as the exemplar for this species. In accordance with the new binomial nomenclatural system, it is proposed that the virus species be called "Caulimovirus dahliae".

Use of conserved genomic regions and degenerate primers in a PCR-based assay for the detection of members of the genus Caulimovirus

The genus Caulimovirus consists of several distinct virus species with a double-stranded DNA genome that infect diverse plant species. A comparative analysis of the sequences of known Caulimovirus species revealed two regions that are conserved in all Caulimovirus species with the exception of Strawberry vein banding virus. Degenerate primers based on these two regions were designed and tested in a polymerase chain reaction-based assay for broad spectrum detection of members of this genus. Cauliflower mosaic virus, Figwort mosaic virus and three distinct caulimoviruses associated with dahlia (Dahlia variabilis) were used to show the utility of this test in detecting diverse caulimoviruses. The primer pair gave an amplicon of expected size (840bp). Amplicons from each virus were cloned and sequenced to verify their identity. The primer pair and the PCR assay provide approach for the broad spectrum detection of several members of the genus Caulimovirus.

Incidence and Relative Prevalence of Distinct Caulimoviruses (Genus Caulimovirus, Family Caulimoviridae) Associated with Dahlia Mosaic in Dahlia variabilis

Dahlia mosaic, caused by Dahlia mosaic virus (DMV), is one of the most important viral diseases of dahlia. Molecular characterization of DMV showed the association of two distinct caulimoviruses (DMV-D10, DMV-Portland) and a D10-like sequence variant (DMV-Holland) with the disease. Using primers specific to these two viruses and the sequence variant, a polymerase chain reaction-based assay was used to determine their relative incidence in several dahlia samples from the United States and the Netherlands. Testing was done on samples collected in 2005 and 2006 in the United States and in 2006 in the Netherlands. Results indicated the predominance of DMV-D10 over DMV-Portland and DMV-Holland in both the United States and the Netherlands. Using conserved regions of the viral genome, primers were designed and used to detect all three sequences. Results suggested that DMV-D10 is predominantly associated with dahlia mosaic, but diagnostics should also include testing for DMV-Portland and DMV-Holland.

Seed Transmission of Dahlia mosaic virus in Dahlia pinnata

Dahlia is an economically important ornamental crop in the United States and several other countries in the world. Among the viral diseases that affect dahlia, Dahlia mosaic virus (DMV) is considered to be the most widespread and to have the greatest impact on flower production. Using grow-out tests followed by polymerase chain reaction (PCR)-based testing of the seedlings, dahlia seed obtained from three different sources were shown to contain DMV. Additionally, the distribution of DMV in various parts of the dahlia seed was determined by PCR. Growout tests revealed a high rate of seed transmission. DMV was detected in cotyledons and, rarely, in the seed coat. The virus also was detected in pollen collected from infected plants. In addition to vegetative propagation, seedborne infection could be contributing to the spread of DMV in dahlia. Use of virus-free seed and vegetative material would result in reduced incidence of the disease.

Genetic Characterization and Real-Time PCR Detection of Burkholderia glumae, a Newly Emerging Bacterial Pathogen of Rice in the United States

Panicle blight of rice (Oryza sativa), caused by the bacterium Burkholderia glumae, is one of the most important new diseases in rice production areas of the southern United States. In this study, pathogenic strains were isolated from diseased panicles in Arkansas rice fields and examined using the Biolog GN microplate system, whole cell fatty acid methyl ester analysis (FAME), rep-polymerase chain reaction (PCR) genomic DNA fingerprinting, and 16S-23S ribosomal DNA (rDNA) intergenic transcribed spacer (ITS) sequence analysis. The B. glumae isolates from Arkansas can be divided into two major groups, but their genetic diversity was relatively low as revealed by 16S-23S rDNA ITS sequence analysis. Since no practical method existed, up to now, for testing the presence of B. glumae in rice seeds, we have developed in this study a real-time PCR method that is effective in detecting and identifying the pathogen in seed lots and in whole plants. The specific PCR primers were designed based on the 16S-23S rDNA ITS sequence of several representative isolates from Arkansas and Japan. This method is highly sensitive, rapid, and reliable, and has great potential for analyzing large numbers of samples without the need for DNA extraction or agarose gel electrophoresis. Although vertical resistance has not been observed among tested rice cultivars, LM-1 and Drew exhibited considerable resistance to B. glumae infection based on disease lesion size and the bacterial growth in planta.

Advances in molecular phytodiagnostics - new solutions for old problems

In the last decade, developments in molecular (nucleic acid-based) diagnostic methods have made significant improvements in the detection of plant pathogens. By using methods such as the polymerase chain reaction (PCR), the range of targets that can now be reliably diagnosed has grown to the extent that there are now extremely few, known pathogens that cannot be identified accurately by using laboratory-based diagnostics. However, while the detection of pathogens in individual, infected samples is becoming simpler, there are still many scenarios that present a major challenge to diagnosticians and plant pathologists. Amongst these are the detection of pathogens in soil or viruses in their vectors, high throughput testing and the development of generic methods, that allow samples to be simultaneously screened for large numbers of pathogens. Another major challenge is to develop robust technologies that avoid the reliance on well-equipped central laboratories and making reliable diagnostics available to pathologists in the field or in less-developed countries. In recent years, much of the research carried out on phytodiagnostics has focussed in these areas and as a result many novel, routine diagnostic tests are becoming available. This has been possible due to the introduction of new molecular technologies such real-time PCR and microarrays. These advances have been complemented by the development of new nucleic acid extraction methods, increased automation, reliable internal controls, assay multiplexing and generic amplification methods. With developments in new hardware, field-portable real-time PCR is now also a reality and offers the prospect of ultra-rapid, on-site molecular diagnostics for the first time. In this paper, the development and implementation of new diagnostic methods based upon novel molecular techniques is presented, with specific examples given to demonstrate how these new methods can be used to overcome some long-standing problems.

Quantitative detection of Cucumber vein yellowing virus in susceptible and partially resistant plants using real-time PCR

A method for the detection of Cucumber vein yellowing virus (CVYV) that combines reverse transcription with real-time PCR (SYBR((R)) Green chemistry) was developed using specific primers designed from a nucleotide sequence of the RNA polymerase gene (NIb) conserved among all the available CVYV strains. This method provided a linear assay over five to six orders of magnitude and reproducibly detected titres as low as 10(3) molecules of the target CVYV cDNA. Real-time PCR gave reproducible results for the quantification of CVYV in young leaves of susceptible and resistant cucumber landraces after mechanical inoculation. Significant differences in the starting amount of target cDNA were found between the analyzed genotypes, indicating differences in viral accumulation that correlated to their different levels of resistance. Real-time PCR results validated our previous findings using slot-blot hybridization, the dominance of the strong resistance to CVYV displayed by C.sat 10, and provided improved reliability and sensitivity of detection. This method has great potential in resistance breeding for germplasm screening, characterization of resistance mechanisms and genetic studies.

Detection and Quantification of Fusarium solani f. sp. glycines in Soybean Roots with Real-Time Quantitative Polymerase Chain Reaction

Fusarium solani f. sp. glycines is the causal organism of soybean sudden death syndrome (SDS). This organism is difficult to detect and quantify because it is a slow-growing fungus with variable phenotypic characteristics. Reliable and fast procedures are important for detection of this soybean pathogen. Protocols were optimized for extraction of DNA from pure fungal cultures and fresh or dry roots. A new procedure to test polymerase chain reaction (PCR) inhibitors in DNA extracts was developed. Novel real-time quantitative PCR (QPCR) assays were developed for both absolute and relative quantification of F. solani f. sp. glycines. The fungus was quantified based on detection of the mitochondrial small-subunit rRNA gene, and the host plant based on detection of the cyclophilin gene of the host plant. DNA of F. solani f. sp. glycines was detected in soybean plants both with and without SDS foliar symptoms to contents as low as 9.0 × 10^-5 ng in the absolute QPCR assays. This is the first report of relative QPCR using the comparative threshold cycle (Ct) method to quantify the DNA of a plant pathogen relative to its host DNA. The relative QPCR assay is reliable if care is taken to avoid reaction inhibition and it may be used to further elucidate the fungus-host interaction in the development of SDS or screen for resistance to the fungus.